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Chapter 27: Amino Acids, Peptides, and Proteins. monomer unit: α-amino acids

Biopolymer: the monomeric amino acids are linked through an amide bond (the carboxylic acids of one AA with the α-amino group of a second)

peptide (< 50 amino acids) protein (> 50 amino acids)

R CO2H

NH2H

!- Amino Acid

R = sidechain

R1

H3N CO2

R2

H3N CO2

+ - H2O R1

H3N

H N

O

CO2

R2

C-terminus

N-terminus

Peptide or protein (polypeptide)

N H

O

R3

H N

O

R2

N H

O

R1

H N

N H

O

R7

H N

O

R6

N H

O

R5

R4 H N

O

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27.1: Classification of Amino Acids. AA’s are classified according to the location of the amino group.

There are 20 genetically encoded α-amino acids found in peptides and proteins

19 are primary amines, 1 (proline) is a secondary amine 19 are “chiral”, 1 (glycine) is achiral; the natural configuration of the α-carbon is L.

!-amino acid (2-amino carboxylic acid)

C CO2HH2N

H

H

C CO2HC

H

H

H2N

H

H

C CC

H

H

H2N

H

H

CO2H

H

H

"-amino acid (3-amino carboxylic acid)

#-amino acid (4-amino carboxylic acid)

CO2H

CH3

H2N H

CO2H

R

H2N H

L-alanine

CHO

HO H

H OH

CH2OH

CHO

H OH

HO H

CH2OH

L-erythroseD-erythrose

CO2H

H2N H

H OH

CH3

CO2H

H2N H

H3C H

CH2CH3

L-theronine (2S,3R)

L-isoleucine (2S,3S)

CHO

CH2OH

H OH

D-glyceraldehyde

CHO

CH2OH

HO H

L-glyceraldehyde

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309

α-Amino acids are classified by the properties of their sidechains. Nonpolar:

(S)-(+)-Valine (Val, V)

(S)-(–)-Tryptophan (Trp, W)(S)-(–)-Proline (Pro, P) (S)-(–)-Phenylalanine (Phe, F)

COO–

NH3

H

N

H

COO–

NH3

COO–

NH3

COO–

NH3

NH3

COO–

COO–

(2S,3S)-(+)-Isoleucine (Ile, I)

(S)-(+)-Alanine (Ala, A)

(S)-(–)-Leucine (Leu, L)

Glycine (Gly, G)

NH3

COO–

COO–

NH3N H

NH3

COO–S

(S)-(–)-Methionine (Met, M)

Polar but non-ionizable:

(S)-(+)-Glutamine (Gln, Q)

H2N

O

NH3

COO–

(S)-(–)-Tyrosine (Tyr, Y)(2S,3R)-(–)-Threonine (Thr, T)(S)-(–)-Serine (Ser, S)

COO–

NH3

COO–

NH3

COO–

NH3 NH3

COO–

NH3

COO–

O

H2NHS

HO

OH

HO

(R)-(–)-Cysteine (Cys, C) (S)-(–)-Asparagine (Asn, N)

pKa ~ 13 pKa ~ 13

pKa ~ 8.2

pKa ~ 10.1

310

Acidic:

Basic:

(S)-(–)-Histidine (His, H)

NH3

COO– COO–

NH3 NH3

COO– N

H

N N

H

H

(S)-(+)-Lysine (Lys, K) (S)-(+)-Arginine (Arg, R)

pKa ~ 10.5 pKa ~ 6.0 pKa ~ 12.5

H2N

N H H

H3N

-O

O NH3

COO–

(S)-(+)-Aspartic Acid (Asp, D)

COO–

NH3

O

-O

(S)-(+)-Glutamic Acid (Glu, E)

pKa ~ 3.6 pKa ~ 4.2

27.2: Stereochemistry of Amino Acids: The natural configuration of the α-carbon is L. D-Amino acids are found in the cell walls of bacteria. The D-amino acids are not genetically encoded, but derived from the epimerization of L-isomers

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311

27.3: Acid-Base Behavior of Amino Acids. Amino acids exist as a zwitterion: a dipolar ion having both a formal positive and formal negative charge (overall charge neutral).

CO2H

R

H

H2N CO2

R

H

H3N _+

Amino acids are amphoteric: they can react as either an acid or a base. Ammonium ion acts as an acid, the carboxylate as a base.

Isoelectric point (pI): The pH at which the amino acid exists largely in a neutral, zwitterionic form (influenced by the nature of the sidechain)

pKa ~ 5 pKa ~ 9

CO2

R

H

H3N _+CO2H

R

H

H3N +

CO2

R

H

H2N HO

_

pKa2 low pH high pH

_H3O +

pKa1

Table 27.2 (p. 1115) & 27.2 (p. 1116)

312

pI = pKax + pKay

2

CO2

CH3

H

H3NCO2H

CH3

H

H3N

low pH

CO2

CH3

H

H2N + +

high pH

pKa1 (2.3)

pKa2 (9.7)

CO2H

CH2

H

H3N

CO2H

pKa3 (3.6)

CO2

H

H3N

CH2

CO2H

CO2

H

H3N

CH2

CO2

pKa2 (9.6)

pKa1 (1.9)

CO2

H

H2N

CH2

CO2

low pH high pH

CO2H

(CH2)4

H

H3N

NH3

pKa2 (9.0)

CO2

H

H3N

(CH2)4

NH3

CO2

H

H2N

(CH2)4

NH3

pKa3 (10.5)

pKa1 (2.2)

CO2

H

H2N

(CH2)4

NH2

low pH high pH

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313

Electrophoresis: separation of polar compounds based on their mobility through a solid support. The separation is based on charge (pI) or molecular mass.

+ _

_ _ _ _ + + + +

+ _

314

Strecker Synthesis: recall reductive amination

C CO2HR

O NH3

C CO2HR

NH2

H

NaB(CN)H3

R C CO2H

NH2

H

C HR

O NH3

C HR

NH2 NaC!N

N!C:

R C C!N

NH2

H

H3O +

-or- NaOH, H2O

R C CO2H

NH2

H

Amidomalonate Synthesis: recall the malonic acid synthesis

H CO2Et C

CO2EtHN EtO Na

RCH2X

H3O

- CO2 RCH2 CO2H C

HH2N

O

RCH2 CO2Et C

CO2EtHN

O

R-CH2-CO2H R C CO2H

Br

R C CO2H

NH2 Br2, PBr3 NH3

H H

27.5: Synthesis of Amino Acids:

Ch. 19.16

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315

R CO2

H3N H H3C O CH3

O O

base R CO2H

HN H

O

H3C

HOCH2CH3

H+R CO2CH2CH3

H2N H

27.6: Some Biochemical Reactions of Amino Acids. Many enzymes involved in amino acid biosynthesis, metabolism and catabolism are pyridoxal phosphate (vitamin B6) dependent (please read)

NH3

R CO2 -

H

L-amino acid

NH3

R H CO2

-

D-amino acid

racemase, epimerase

H3N

R H

H

decarboxylase

O

R CO2 -

transaminase

N

2-O3PO OH

O H

pyridoxal phosphate (PLP)

+

N H

PO

N

OH

CO2 -R

27.5: Reactions of Amino Acids. Amino acids will undergo reactions characteristic of the amino (amide formation) and carboxylic acid (ester formation) groups.

316

27.7: Peptides. Proteins and peptides are polymers made up of amino acid units (residues) that are linked together through the formation of amide bonds (peptide bonds) from the amino group of one residue and the carboxylate of a second residue

By convention, peptide sequences are written left to right from the N-terminus to the C-terminus

H2N CO2H

Alanine

H2N CO2H

HO

Serine

+ - H2O H2N

H N

O

CO2H

OH

Ala - Ser (A - S)- H2O

H2N

H N

O

CO2H

HO

Ser - Ala (S - A)

C-terminus

N-terminus

C-terminus

N-terminus

N H

O

R3

H N

O

R2

N H

O

R1

H N

N H

O

R7

H N

O

R6

N H

O

R5

R4 H N

O

backbone

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317

The amide (peptide) bond has C=N double bond character due to resonance resulting in a planar geometry

restricts rotations resistant to hydrolysis

R1

H N

N

O R2 H N

O

amide bond

R1

H N

N

O R2 H N

O

_

+

H H

The N-H bond of one amide linkage can form a hydrogen bond with the C=O of another.

N

N

O

H

R

O

H

N

N

O

H

R

O

H

N

N

O

H

R

O

H

N-O distance 2.85 - 3.20 Å optimal N-H-O angle is 180 °

Disulfide bonds: the thiol groups of cysteine can be oxidized to form disulfides (Cys-S-S-Cys)

SH HO2C

NH2 2

1/2 O2 H2O

S HO2C

NH2

S CO2H

NH2H2

318

N H

O

R2

H N

O

R1

N H

H N

O

R5

N H

O

R4

H N

O

N H

O H N

O

R6

N H

H N